Research workbench
Crystal structure of fcrn bound to ucb-303
Analyse Crystal structure of fcrn bound to ucb-303 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C99
- Type
- protein
- Length
- 723 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG receptor fcrn large subunit P51; Beta-2-microglobulin
- UniProt
- P55899, P61769
- Ligands
- EQY, NAG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IgG receptor fcrn large subunit P51 | protein | 265 | 26% helix, 41% strand | P55899 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | IgG receptor fcrn large subunit P51 | protein | 260 | 26% helix, 41% strand | P55899 |
Ligands and binding sites
- EQY · Methyl 7-(3,5-difluorophenyl)-5-(pyridin-3-yl)[1,2, 4]triazolo[1,5-a]pyrimidine-6-carboxylate · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
- CIT · Citric acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.74 | 0.77 | 116 | EQY, GOL |
| 2 | 189 | 0.47 | 0.75 | 29 | empty |
| 3 | 142 | 0.46 | 0.77 | 20 | GOL |
| 4 | 111 | 0.37 | 0.74 | 21 | empty |
| 5 | 84 | 0.31 | 0.73 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1518 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1348 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 958 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 87 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6C99 · Crystal structure of FcRn bound to UCB-303 · the same entry in another collection · chain D against D, TM-score 1.00
- P55899 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P55899) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P55899
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6C99 · PDBe 6C99 · UniProt P55899 · UniProt P61769
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